The link type is relevant because a web link looks like this... https://www.evernote.com/shard/s2/nl/120918/84f36e9b-ab86-3e88-6462-- etc.... and an app link is evernote:///view/120918/s2/84f36e9b-ab86-3e88-6462-7ee0bae3b2a6 etc... and only a browser can open the first one. The second one calls the installed app and adds a note reference. I highlighted part of the link because clearly this is the note UI. The link prefix determines where and how it opens - or doesn't - as the case may be.
Clipper has also changed in that clipping a web page defaults to being done server-to-server with the synced note then being able to display in the app if that's what you require.. although since Elektron came in the difference is almost academic in that the 'installed' app comes with a built in browser wrapper.
Not sure if it still applies to Evernote, but there used to be a Windows protocol that if an app was installed locally the user would be asked whether you wanted to have links open in the app or the browser, and that setting would be maintained by a local cookie but I think that was before the link style changed to this format.
As I said to the OP here - if you're getting misfires when following links, it's probably best to go for a clean complete reinstall - I mainly use app links (I'm mainly desktop based these day) and I've had no trouble with links in my very large account over the past several years. You could also reinstall Clipper to make sure you have the latest version in case that's a factor.
If you are using the old Legacy app - remember that there's now a translation back-and-forth when viewing notes in both that and the new version. If it appears that opening a note didn't work - could that be due to a long(er) translation time on some notes.